Network Inference

The CLR algorithm

CLR infers regulatory interactions between transcription factors and their targets using a compendium of gene expression profiles

Faith JJ, Hayete B, Thaden JT, Mogno I, Wierzbowski J, Cottarel G, Kasif S, Collins JJ, Gardner TS. Large-scale mapping and validation of Escherichia coli transcriptional regulation from a compendium of expression profiles. PLoS Biol. 2007 Jan;5(1):e8.[html]

The CLR algorithm may be downloaded and used freely for non-profit use. Commercial users please contact Tim Gardner.   [Download]

Published network inference datasets

Modi, Sheetal R., Camacho, Diogo M., Kohanski, Michael A., Walker, Graham C., and Collins, James J. Functional characterization of bacterial sRNAs using a network biology approach. PNAS. 108(37):15522-15527. 2011. [html] [Download dataset]